


A Day in the Life of Dr. Rafael Esquivel, Ph.D.

by White Aster (white_aster)



Category: Transformers - All Media Types, Transformers: Prime
Genre: Episode Style, Gen, Gen Fic, Post-Canon, Science
Language: English
Status: Completed
Published: 2011-07-15
Updated: 2011-07-15
Packaged: 2017-10-21 10:05:26
Rating: General Audiences
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 9,088
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/223985
Author URL: https://archiveofourown.org/users/white_aster/pseuds/White%20Aster
Summary: <blockquote class="userstuff">
              <p>Someone needed a nanite specialist.  Someone kidnapped the best.</p><p><i>This, Raf thought, is my life: staring down beings who're at least ten times my size, think they know everything, and have no eyeballs.</i></p>
            </blockquote>





	A Day in the Life of Dr. Rafael Esquivel, Ph.D.

_(Set...I 'unno, 20, 25 years or so post-series, so when Raf is mid-late thirties.)_

\---------

Dr. Rafael Esquivel, Ph.D. was no more a morning person than little Raf Esquivel had been at twelve. His lab could vouch for that, having shared rooms at conferences with him and, in one memorable instance, having to literally drag him from bed to give a 9:30am talk. Raf knew his weakness and tried to compensate. He set three alarms, of increasing levels of loudness and in increasingly difficult-to-reach places. Usually, by the time the third alarm went off like an air-raid siren on the other side of the room, he was capable of stumbling over to turn it off and not immediately falling over again. Usually. This was not to say that he was, strictly, AWAKE. THAT was reserved for after he'd had a chance to down his triple-shot latte from his favorite indie coffee shop on the way to the lab.

Still, he could function. He could gather his things, grab his bag, and cross the street to the deserted bus stop without incident. He just wasn't at his sharpest.

Which was probably why, when a Decepticon descended out of the sky to land with a crunch of concrete next to him, Raf's only, wholly uncaffeinated response was to blink up and say, "....ur?"

Dr. Esquivel was scooped up as easily as any twelve-year-old.

Three minutes later, the bus trundled by the empty stop.

\-----------

Raf had learned early on that there were several pro tips to follow when physically dealing with Cybertronians. One was, of course, to watch where you were walking, as they had a considerably harder time keeping track of you than you did of them. Another (dubbed "The Miko Rule") was, should a Cybertronian pick you up, to not make any sudden moves that might make them drop you.

Raf totally had that one down.

As Raf watched the ground drop away from him at an alarming speed that was doing a better job than his usual latte of cutting through the morning sleep fog, he reminded himself of the very first rule: Don't Panic.

Then they did a slight roll, wind whipping around them as they changed direction, and Raf closed his eyes in sheer self-defense, hands clenching against the metal fingers that held him. He was fine with heights! Really! Just...not quite THIS high.... You know...without an airplane....

Over the sound of the rushing wind, Raf heard, right next to his ear, "Do not move."

His eyes popped open in surprise, then immediately screwed shut again, but before he could ask what or why or where the hell he was supposed to move TO, the spindly grip on him shifted, the press of upward lift easing and the sound of transformation suddenly loud in his ears. Sound and wind did a strange dance around him, and then the wind was gone, replaced by the hum of engines, and Raf was pressed down by gravity into a...seat?

Cautiously, Raf opened his eyes, and found himself in the cockpit of a very small and, by the speed the ground was moving far below them, very FAST, plane. With a very disconcertingly clear view of the drop beneath him. Raf gulped and wondered if his brain had been left somewhere at the bus stop. "Did...did you just transform AROUND me?"

A small video screen set into the controls in front of him flickered with green text: AFFIRMATIVE.

"Okay. Just...checking," Raf said, swallowing. It had been a long time since he'd seen any of the Decepticons up close. Ten years, at least? Not that they, along with the Autobots, weren't all over the news whenever they were caught on camera, but that didn't happen much with the Decepticons. They'd been fairly quiet, preferring their usual hit-and-run tactics or battles far away from human interference. Still, Raf would never forget that faceplate, though the frame had been a bit different than he'd remembered. "Okay...so...Soundwave, right?"

AFFIRMATIVE.

"Right. So, uh. Gonna tell me what this is about?"

YOUR ASSISTANCE NEEDED.

"O...kay." Something hard (probably his water bottle) was jamming into the small of his back. Raf wondered if he dared shift to try to get his backpack off. But then, if Soundwave was going to transform around him again, he didn't want to have to worry about dropping it.... _Not,_ he thought, that that's my biggest concern at the moment. Oh man, I've been kidnapped again. I'm too old for this.... Miko's gonna laugh.

Still, evidently being an Autobot ally was like riding a bicycle: you never really lost the knack. Or the rusty but familiar checklist of What To Check When Kidnapped: he was safe. He was unharmed. He wasn't entirely sure where he was (other than INSIDE SOUNDWAVE...Raf quickly veered away from that panic-inducing thought), though they were heading...north...ish. He had his cell phone and laptop but...probably couldn't call for help unless Soundwave wanted him to. This WAS Soundwave, after all.

Overall, Raf told himself, things could be worse. No, really. He took a deep breath. "Where are we going?"

That didn't get a response. Well, fine, then.

"What kind of assistance do you need?"

A pause, then: EXPERT TECHNICAL ASSISTANCE IN CYBERTRONIAN NANITE ENGINEERING.

Raf blinked. He supposed that it was pretty obvious to a Decepticon that his nanotechnology research was based on Cybertronian nanites. But...they weren't exactly new. The Cybertronians had been using them for autorepair for longer than the Earth had been habitable. Surely the Decepticons still had a medic? What was his name, the red one...Knock Out. "What happened to your medic?"

Silence. Well...blank screen.

Raf sighed, his ears popping. He let himself relax back into the seat, just a little. "If all you needed was some help, you could have asked, you know." He probably would have even helped, so long as it didn't hurt anyone else. After all, if it was so dire they needed to go to a HUMAN for help....

POINTLESS. REFUSAL NOT AN OPTION.

 _Juuust in case I forgot I was dealing with a Decepticon...._ "...right. Well, so long as we've got that cleared up."

Raf let it go and looked out the window. Below them, dusty brown desert was rapidly falling away to mountain forest. Were they at the Rockies, already? They were heading straight north now. How fast could Soundwave GO? Raf eyed the altimeter, then the speedometer. Damn, they could be in CANADA already. He was just trying to remember how far it was to the border when Soundwave dove.

Raf's stomach rolled and his heart flew up into his throat, making him swallow an embarrasingly unmanly noise of surprise. His hands flew to the wheel simply for something to hold on to as they rapidly lost altitude. "This is on purpose, right?"

The engines' hum changed, and Raf felt the forward-press of lost speed. They crested another mountain, white-topped and its sides furry with evergreens, and Raf knew they'd arrived.

Nestled in a valley surrounded by snow-capped peaks, a slight gouge in the rocky soil trailing behind it, was the Nemesis.

Soundwave circled a few times, dropping below the mountaintops until he hovered just above the ground. Raf tore his eyes away from examining the Nemesis' hull. "Wait, I can get out on myYAAAAAAH!" Too late. The engines cut out, and the sound of invisible joints unlocking and metal sliding was Raf's only warning before the seat shifted underneath him and the cockpit cracked open over his head. Raf gritted his teeth, following The Miko Rule until the world stopped spinning.

He opened his eyes again to find that even as a grown man, being held in a twenty-foot tall cybernetic organism's hand was a disconcerting experience. That wasn't what caught Raf's attention, though.

It was quiet. Very quiet. The valley was secluded, not much larger than the Nemesis itself, and probably completely inaccessible by any route but air. (Or landbridge, he reminded himself. That last bit made Raf feel a bit less like he was off the map.)

Raf looked around, cold mountain wind ruffling his hair, then realized that he had TIME to look around, and looked up at Soundwave.

The Decepticon just stood, head turned toward the Nemesis. Then, a spike of something flowed across his faceplate, and he looked up. Raf followed his gaze, squinting against the bright blue sky, and thought that he could just make out what might have been a formation of planes, high above.

There were no other Decepticons in the valley. The Nemesis itself, Raf realized, wasn't even making any noise: no hum of engines, no indication of activity...nothing. It was like a ghost ship.

Raf stood, slowly, balancing with old instincts on the uneven surface of Soundwave's palm. "Something's wrong," he murmured.

Soundwave looked down at Raf, words flowing across his faceplate: HOLD ON.

Raf obediently wrapped an arm around one of the slender fingers cupped around him, and Soundwave stepped forward.

\----------

Raf never would have said that he was FAMILIAR with the interior of the Nemesis. He'd been inside the Decepticon warship a few times, sure. Briefly. And usually due to accident or desperation. Certainly never under conditions that lent themselves to in-depth study.

Now, though, as Soundwave's steps clanked purposefully on the Nemesis' deck plating, Raf's initial sense of WRONGNESS just got worse. The entire ship was nearly silent except for a slight, almost subharmonic hum that Raf always associated with charged energon lines. Probably the basic power system that was keeping the lights on and the doors responsive, he figured. Whatever was wrong, the ship seemed perfectly intact.

There were still no signs of life. No one passed them in the halls. No voices echoed from further in the ship. Raf had always thought the Nemesis a little deserted. He'd gotten the impression that the warship was built for a much bigger crew than he'd ever seen man it, but this...this was worse. This wasn't just understaffed. This felt ABANDONED. It made the whole ship yet more alien and was extremely creepy.

"Where is everyone?" Raf finally asked, even his hushed, human-sized voice bouncing off the metal walls.

Soundwave didn't answer, just continued through another door into a room with several holo-monitors. He lowered his hand to the console, flattening his curled fingers down in clear invitation, and Raf stepped off, carefully avoiding any of the buttons and dials while trying NOT to look like he was trying to decipher every Cybertronian glyph he could lay eyes on. From what he could see, this was...some kind of internal surveillance station?

 

The monitor flickered as Soundwave tapped a few buttons, cycling through what looked like several security cameras. They all showed empty halls. In some places, it looked as if there'd been something of a panic. A cargo bay that showed signs of a fight, complete with laser burns on the floor and what looked like spatters of energon. One room with tables and chairs looked like a herd of something had gone through and no one'd cared: chairs overturned, a few tables askew.

Raf shook his head, turning to look at Soundwave and just demand to be told what the hell was going on. Before he could say anything, though, Soundwave pointed back at the monitor. Raf's words died in his throat as he saw what was there.

The camera shot was of some kind of long, bare hall. A storage room or cargo bay of some sort. It was filled with Decepticons. Mostly Vehicons, but also more specialized mechs. Raf was fairly sure he recognized Breakdown propped against one wall and a few other mechs scattered about, but he couldn't find Megatron or Starscream. Still, there were hundreds of them, lined up on the floor or dumped in chaotic piles. Some of them were missing hands or feet, some streaked with some dark char or showing shiny fresh welds. Had there been a battle? It reminded Raf chillingly of the war footage on TV, of bodies lined up for identification....or piled for mass burial.

None of the Decepticons were moving.

"Are they dead?" Raf asked, quietly, squinting at the footage.

Soundwave made a complicated but generally negative hand motion, then adjusted the camera, zooming in on one of the Vehicons until Raf could see the mech's damage. He thought for a moment that this mech had both the char damage and welds, but as the camera zoomed in, he realized what he was seeing. The dark patches were not soot. They were holes eaten in the metal of his plating, leaving gaping wounds over his internals. What Raf had taken for welds due to their shine were actually wounds in progress: places where the decay was already underway and had eaten through colored outer plating to the raw living metal underneath. It looked like nothing so much as acid damage, but surely the Decepticons could deal with that. How was this--

The view on the monitor zoomed in on the Vehicon's hand, or what was left of it, the image breaking apart to show a structure that Raf saw in his sleep: a mostly-Cybertronian autorepair nanite but with very, very familiar modifications. "No. Oh no," Raf breathed.

The magnified image changed, to something that looked like a real-time electron micrograph: jagged metal edges swarming with nanites, an advancing army devouring as they moved methodically forward.

Raf clenched his hands until they hurt, joints creaking. "No!" He craned his neck up to look at Soundwave. "You're fucking kidding me!"

Soundwave just looked at him, then pointed to the screen.

Raf dragged his hands through his hair. _This can't be happening. Oh god, please let this be a nightmare...._ "How did they get here? They're experimental! And besides, this...this isn't what they do at all! They're programmed to accelerate healing, not destroy! I've TESTED them. There's no WAY they could be doing this, unless--"

He stopped, looking back at the screen, at the great gaping holes in armor and plating and circuitry. "Unless someone reprogrammed them," he whispered. He leaned forward on the console, head hanging. "Oh God. But how...it's Cybertronian tech, no one should...wait." His head snapped up, turning to look at Soundwave. "It wasn't you guys, was it? PLEASE tell me you weren't stupid enough to...to get ahold of them and try to tinker."

"No," Raf's own voice spoke back to him, sketched in the jumping line bisecting Soundwave's faceplate.

"Good. Good." Raf looked back at the console, at five years of work eating its way through the Decepticon army. He was suddenly glad he'd never eaten the breakfast he'd stashed in his backpack. He felt like throwing up. Decepticons were Decepticons, but...no one deserved this. The thought that he'd been responsible for it made him sick.

 _Focus, Rafael. Focus._ That internal voice sounded a lot like Ratchet.

Ratchet. There was an idea. Sure, Ratchet couldn't come here, even if Soundwave would let him. There was no way Raf wanted any Autobot anywhere NEAR this place. But he could consult, at least, and he had as much access to Raf's lab as Raf did. Just by being on the ship Raf was probably exposed. He wouldn't be able to leave. He'd need to work from here...jury up something that could analyze the nanites' programming as well as the equipment in his lab. God, the lab. Had there been a security breach? How did the nanites get out? How did enough of them get out to do this much damage? They couldn't reproduce...HIS version couldn't reproduce, and god, he hoped THESE couldn't reproduce...so it must have taken a huge dose to do this. Where did it come from? How were they exposed? He couldn't imagine an accident that could do this. It must...god, it must have been a weapon of some kind. Who could have done it? Who was using his research for this?

 _Focus. One thing at a time. Save lives first. Kick ass later._

Raf took a deep, steadying breath, shoving his anger way down. He straightened, turning to face Soundwave. "Ok. Ok, here's what I need."

\--------

It took a bit of a staring contest, but eventually Soundwave picked Raf up and took him through several doors and hallways, up in a lift, and then into a large room rounded in holoscreens. Raf squinted, trying to read the glyphs there (there were some definite differences between Decepticon and Autobot glyphs that always made him wish that he had another life to be a linguist), but Soundwave set him down right by the door, pointing one skeletal finger at Raf in a silent "Stay". He moved over to one of the stations and did something that made a few sectors of a holoscreen blink.

Coming back, Soundwave picked Raf up, repeating Raf's own words, "Contact Ratchet," as he walked them back out.

Raf pulled his cellphone out of his pocket, hitting speed dial without even looking.

Ratchet picked up before it even rang. "Rafael! I thought our conference call wasn't until ten."

Raf looked at his watch. It had been only a little over an hour since Soundwave had picked him up. His lab probably didn't even know he was missing yet. "I'm fine, Ratchet. I'm on...ok, before I say this I need you to not freak out, ok?"

"...what did you do?"

Raf chuckled weakly as he settled his headset in his ear and stuffed his phone back in his pocket. Lord knew he had heard that tone and seen the suspicious face that went with it enough times when he was young. "Nothing. Soundwave came and...picked me up." Technically true, he supposed. It was certainly a less loaded word than "kidnapped". "I'm on the Nemesis, and we've got a big problem. Someone's gotten ahold of the nanites and turned them loose in here. I don't know how they got here yet or where they came from, but there's something wrong with their programming. They're eating through armor plating, circuitry, everything. They've probably contaminated most of the ship. Most of the Decepticons are--AAAGH!" He jerked, clawing the headset from his ear as feedback squealed over the line. "What the--"

They had stopped in the middle of the hall. A spindly finger waved in front of him in a "no no" gesture, and Raf looked up at Soundwave, brow furrowed. "Oh, come ON! What, you don't want him to know how bad it is? I think he can figure it out! Otherwise you never would have come to me!" Raf banged a fist against Soundwave's nearest finger (it felt like thumping a steel girder) and planted his hands on his hips. "Look. You want my help, Ratchet's part of it. I'm just an engineer. HE's the medic. And there's no way he can help if he doesn't know the situation. Now if you want me to do my best, quit screwing around!"

This, Raf thought, is my life: staring down beings who're at least ten times my size, think they know everything, and have no eyeballs.

Soundwave's faceplate spiked soundlessly once, and Raf could hear the feedback clearing from the phone line.

"--ael! So help me Primus, Soundwave, if you hurt him I will turn you into--"

Raf got his earpiece back in and shouted over Ratchet's indignation as they continued moving again. "It's ok! It's ok, I'm here. I'm fine. We were just having...a difference of opinion. All cleared up now."

Ratchet harrumphed. "Well. Fine. Tell that Decepticon that if he interferes with the line again I'm going to consider it an act of war, and to the Pit with whatever backroom deal Prime and Megatron have going."

Soundwave's faceplate blipped a small, somewhat derisive spike.

"Yeah, he hears you. Look, Ratchet, back to the nanites...."

"Right. Fine." Ratchet sighed over the line. "You said that they'd contaminated the ship? How is that even possible? How did they get out of the lab?"

"I don't know. Whatever turned them evil must have killed their self-destruct programming, or programmed them for reproduction. I mean, somehow they've spread to...a hell of a lot of mechs. They've got to be crawling all over this place." Raf rubbed his arms. It was like his microbiology class in undergrad: sure, he knew that there were bacteria all over him and that they were harmless, but it still made his skin crawl.

"Then you and Soundwave are probably carriers."

"Yeah. I'm going to have to work from here. I've got my laptop with me, at least, and...well, there has to be a medbay here somewhere. Maybe I can use the same buffer emulators I use to interface with your tech to get access to the scan data. Once I see a full scan of the nanites and can access their coding, I can see what's wrong." Raf looked up at Soundwave, who nodded and picked up his pace. "Soundwave showed me what looked like some preliminary scans. Maybe they already tried to diagnose it before they got too sick."

"Well, send me what you can. What do YOU need?"

"I need you to send me the latest full working copy of the nanite code. It's in the usual place on the server. Just updated it last night. The basic buffer emulator program is on my laptop....I don't know other than that. It depends how much I can patch into the medbay computers--whoa!" Raf tumbled a bit in the upturned cage of Soundwave's hand as they made a sharp turn. Raf crouched down to lower his center of gravity, grabbing onto one of Soundwave's fingers for balance. "I might have problems connecting to the nanites. Hopefully I won't need to get the specialized equipment from the lab, but I don't know what their computers can do here. If they've got autorepair calibrators, I might be able to use those." He looked up at Soundwave. "I guess it's too much to ask that your medic's awake?"

A door swept open in front of them, and Raf recognized the Decepticon medbay where Megatron's comatose body had laid so many years ago, mostly because Megatron was in the same place, his body surrounded by a curtain of blue light. The holes weren't just in his chest this time, instead riddling his plating like swiss cheese. Rafael saw, queasily, that it looked like Megatron's right hand below his cannon was completely gone, and his right leg worn down to the struts. The damage looked almost like he'd been splashed with acid as the nanites ate away at his frame.

Soundwave was pointing otherwhere, though. Rafael tore his eyes away from the damaged Decepticon leader and saw that there were more examination tables, each with a mech on them. Rafael recognized Starscream, Thundercracker, Knock Out...the officers, he realized. They all also showed signs of nanite infection, with Starscream the worst off. His arms were missing most of the way to his shoulders, and streaks of plating were missing everywhere Raf looked. The others looked almost as bad, with missing hands or feet. It made sense...they'd probably picked up the nanites predominantly from surface contact. He looked at Knock Out, who had one finger left on each hand and a lot of damage around his upper arms and torso. Raf could see what might have been sparklight flickering in the depths of his chest like a heartbeat. Yeah, so much for having a medic's opinion.

Raf pointed at the blue fields surrounding every table. "Stasis fields?"

Soundwave nodded as he took Rafael over to one of the consoles.

"What type of stasis field?" Ratchet asked.

"Blue kind. Full temporal subspace field, Ratchet." Raf followed Soundwave's motions as he accessed the files, pulling up graphs. Raf puzzled out the axes, then the timestamps. "Yeah, that works. The fields have halted the nanites. It'll give us some time, at least. Well, for these guys. It looks like they've only got the officers in here. There's a cargo bay full of others that might not be so lucky."

"In their defense," Ratchet said, grudgingly, "Full subspace fields of a size to fit an entire mech are incredibly resource-intensive. They probably don't have the power reserves."

"Still doesn't seem fair," Raf muttered, trying to wave Soundwave's fingers away from the console controls. "Hey, you shouldn't be touching things in here. You probably shouldn't even be STANDING in here. This place is probably crawling with them."

Soundwave pulled his hands back, but otherwise didn't move.

"Don't trust me alone in here, huh?" Raf squinted up at the holoscreen, then cracked his knuckles and began the acrobatic process of inputting on a keyboard that was definitely NOT human-sized. The glyphs were kind of like him trying to read Portuguese: very similar to a language he knew, but enough to slow him down. "Oh god, acronyms, great. Fine. You can stay and translate for me."

"I've got the code, Rafael. Where do you want it sent?"

"Just send me an email, I guess. I know, I know, Agent Lightner would explode about insecure connections, but I don't have any choice right now."

"Sending. Anything else?" Ratchet said.

Raf gritted his teeth. "Speaking of Agent Lightner, you can call her and General Morshower, tell them there's a security breach, and get them started on finding out who the hell stole my work. Call Jake and Penny in the lab, too. Half of this coding is theirs. They can be pissed about it, too. Tell them to lock down the lab, go back through every log they can think of. The computers, the fabricators, the 'nite stock logs. Everything." His eyes flicked up to the holoscreen, where his creation turned in slow-motion 3D. "I want to know where the hell these came from."

\-------

It was a good few hours before Raf felt he had a handle on the setup available to him. With some creative daisy chaining of adapters and the emulators that Raf used to connect to the Autobot computers, he was able to connect to the Decepticon medbay mainframe.

The medbay scanners were more than capable of giving him beautiful physical scans of the nanites (which were, as Raf had predicted, coating just about every surface in the medbay), which were physically completely identical to those in his lab and NOT to endogenous Cybertronian auto-repair nanites. These had definitely come from his lab, which was frustrating in that he wanted to strangle whoever took them OUT of his lab but reassuring in that he knew them inside out. He even was able to upload the translation programs into the medbay computers to get them to trigger a log and code upload from the nanites.

In the meantime, Raf scanned through the most recent medbay files. Knock Out's professional documentation was dense with medicalese, but between Ratchet and Soundwave's translations, Raf was able to patch together the story of what had happened.

A Vehicon, designation Dropkick, had come back from a mission and presented with plating weakness and general poor function in his left pede servos. He indicated that he'd been part of a classified mission and in the process had come in contact with several barrels of an unidentified human-made substance--

"BARRELS? BARRELS of it?!" Raf said, hands gripping the side of the console hard enough to hurt. "Oh god...."

\--that they had brought back to the Nemesis for analysis. Knock Out noted that he'd ordered Dropkick's entire team and the mystery substance quarantined, but it appeared that it had been too late. The rest of Dropkick's team members were corralled and eventually presented with similar symptoms in varying sites, as did Starscream and Thundercracker, who'd been analyzing the barrels' contents; Megatron, who had been present while they'd done so; Knock Out himself, and eventually other, uninvolved Decepticons. Case numbers bloomed and then cut off as Knock Out curtailed medbay access to deal with the most serious cases and the officers. He identified the agent as an engineered nanite and made headway on isolating and analyzing the pathogen, but at that point, two days post-first-exposure, he had a critically ill command chain. Despite belated decontamination procedures, the nanite had worked its way around and through plating and into internals, where it had wreaked havoc on power, coolant, and circuit systems. At that point, Dropkick and his entire team had offlined, the nanite having made its way through their energon circulation systems to their power plants and from there to their processors.

"Oh god," Raf said, head dropping into his hands. _I'm sorry. I'm so sorry._

Knock Out made several innovative and practically heroic efforts to prevent Megatron, Starscream, and Thundercracker from suffering the same fate, but eventually had no choice but to put the officers in stasis in order to halt the damage. Knock Out ordered the rest of the crew--who had, by then, all been incidentally exposed--put into self-stasis to slow energon circulation and nanite migration.

The logs cut off not long after that, with the last case update being Knock Out's own, where he'd noted he was putting himself into stasis before he couldn't work the controls anymore. The last entry was a video log: Knock Out, as he was on the stasis bed, exhausted and streaked with lost metal. "I've set our beacon to indicate a plague quarantine, and all crew outside the ship have been ordered to not board. Luckily, we've had no recent contacts with Decepticons returning to space, so this agent should be contained to the Nemesis and at the very least to this planet. For now. If this is some weapon--and I can't imagine how it wouldn't be--then we may all see it again, as it is obviously terribly effective. Congratulations to whoever invented it, and may you rot in the Pit. I have sent on a report, including specs on this agent, to our third in command, Subcommander Soundwave, who has escaped contamination. He is in command of the Decepticon army until such time as Lord Megatron and Commander Starscream can be revived." Dark-flecked lips pulled back in a wry, humorless smile. "Long live the Decepticons."

Raf stared at the holoscreen, numb. His hands shook, and it wasn't just because it was freezing in the medbay. Ratchet was saying something, he realized. "S...sorry, Ratchet. What did you say?"

"I said, why is Soundwave there with you if Knock Out said he escaped contamination?"

Raf looked up at the Decepticon. "Yeah. Why did you come back here? Wait...you...." Raf's head felt fuzzy. He needed to eat something. God, what time was it? "You knew what had happened. You had Knock Out's report. And yet you brought me here?"

Soundwave's head tilted, slowly. His faceplate strobed with images: Rafael, at his latest nanotechnology conference, gesturing at his slides. Raf's last publication, on nanite replication. Then, things that Raf knew had never been anywhere but his home or work servers: diagrams from the healing nanite designs, text files of their code....

"So you've been SPYING on me," Raf said, rubbing his temple. "Figures. So what, you figured I'd be able to help?"

The console next to Raf beeped, indicating that the upload of code from the re-engineered nanites was complete. Raf downloaded it to his own computer, then set his text program to identify differences. Then he looked up at Soundwave, who hadn't answered. "Ok, yeah, so I'm helping. Good call, there. But seriously...why would you...." Raf paused in the middle of pulling his water bottle out of his bag. "Because there was no other way to get me here. Well...except maybe tell one of the others who'd been outside to do it. Which probably wouldn't go over too well." He shook his head, opening his water bottle and taking a long drink. "And you...you wouldn't just leave it alone. You could have just...left. Taken command and left everyone here to die. But you didn't."

Soundwave looked at him silently for a moment, then replied in Knock Out's voice, "Third in command...Lord Megatron and Commander Starscream can be revived."

Ratchet's voice murmured in Raf's ear, "He's a good soldier. A Decepticon. But a good soldier."

Soundwave was silent.

Raf looked down at his laptop with new determination. "I've got the code, Ratchet. I'm gonna send it to you so you can--"

Soundwave's hand came down like a striking hawk. Three fingers sank into the deck plating, fingers caging the laptop and missing Raf's arms and legs by inches. One other gave a brittle snap, pieces flying up and hitting Raf's bare forearm.

Raf froze.

"What was that?" Ratchet demanded.

Soundwave's faceplate showed Knock Out: "If this is some weapon--and I can't imagine how it wouldn't be--then we may all see it again."

Raf stared up at him. The place where Soundwave's talon had hit him ached now, and he could feel a warm trickle from what was probably a small cut. He didn't move, watching energon start to seep around where Soundwave's broken finger was digging into the floor. Raf could see the telltale mottling and pocking above the break. The nanites hadn't eaten through the digit (yet), just weakened it.

They both, for a long moment, just bled onto the Nemesis' deck plating.

"I guess I can't blame you," Raf whispered. "No. You're right. It's too dangerous."

"Rafael?" Ratchet sounded worried.

Raf held Soundwave's...faceplate. "It's ok, Ratchet. I'm gonna try fixing this myself. I've got an idea."

"Why does that not reassure me, Rafael?"

Soundwave lifted his hand out of the way. Raf checked his arm (just a scratch, really, not even bleeding much) and grabbed and tore the wrapper off his breakfast bar. God, he was starving.

"Because, Ratchet," Raf said, through a mouthful of granola, "you have too little faith in my genius."

\---------------

"Well, we can scratch Penny and Jake off the suspect list," Raf said some time later, stretching. "This code is UGLY. Both of them are better than this. Whoever reprogrammed these little guys barely knew what they were doing."

Penny, from the little video conference window in the corner of his screen, snorted. She turned to face her webcam. "Like I'd sell you out. I'm a POSTDOC. What would I do with MONEY?"

Jake piped up from his own window, "I could think of a few things. I totally won't work with anyone but Raf, though. I've got STANDARDS."

Penny grinned, not looking away from her furious typing. "See, Raf, if you ever turn evil, you'd come with your own comic relief sidekick. Whoa, hello." She squinted at something on her screen. "Raf, I got the server logs. There are a few incursions I don't recognize. Definitely someone trying to cover their tracks. And they did download a good bit of data...about two months ago. Wait is this...crap, TWO incursions, though this one's more a backdoor...ongoing contact, last one was yesterday...don't think they copied anything...and wow...I've never seen anything like this code. It's not the usual hacker cut and paste...WOW. SHINY. Here, Raf, take a look."

Raf spared a second from watching the repaired nanite code compile. He pulled up the attachment and scanned it. He whistled. "Yeah, that's....NOTHING like anything I've seen. Not the way anyone else does backdoors at...all. ...wait." He looked up at Soundwave, suspiciously. "Let me guess." He pointed at his screen, raising an eyebrow questioningly.

Soundwave replied with Penny's voice, "SHINY."

Raf snorted. "Ok, ignore the backdoor, Penny. For now. S'not what we're looking for."

"Okay. Whatever you say. Friend of yours?"

"Professional acquaintance."

"Well, tell him I'm gonna steal his code. Don't know what I'm gonna USE it for, but I'm totally stealing it."

"I doubt he wants royalties, Pen. Can you tell if the other guy got the nanite code?"

"I can't really tell, but the file sizes are about right. I'd bet a pitcher of beer on it."

"All right. Forward that on to Agent Lightner. She can track it down." Raf's eyes switched windows. The changes he'd made to the nanite operating code had come back clean. He took a deep breath. "Guys, I'm going to hang up here. Gotta concentrate."

He'd told them about the security breach, the altered code. NOT that he was sitting on a warship full of Decepticons that he was trying to save. Raf was pretty sure they thought he was on assignment wherever the nanites had showed up. He'd managed to avoid having to give them a location. There was no reason to link his students with the Decepticons anymore than he already had, but Jake and Penny weren't stupid. They knew that the "Ratchet" they sometimes audio conferenced with was not just some spook with a code name. They knew something was up. Raf could tell by the look they shared over their shoulders. They both looked very young, all of a sudden, and Raf was struck with a wave of affection for them.

"Be careful, Raf," Jake said, unusually serious. "And hey, whatever dudes are there with Raf? Bring our PI back in one piece! We kinda need him!"

Penny rolled her eyes. "Let us know if you need anything else, Raf."

Raf smiled. "I will. I'll call back in a bit." _Hopefully. We haven't exactly negotiated what happens if I manage to fix this, have we? Or if I don't._ Raf shoved the thought away and cut the connection.

He blew out a breath and checked his watch. Nearly dinner time. Unfortunate that he didn't have any dinner. "If this doesn't work," he said to his looming guardian, "you're gonna have to order delivery or something. My granola stash is all gone, and I haven't figured out how to process energon yet."

Raf stood, knees creaking from sitting on the hard floor for hours. He looked at the laptop in his hands and paused, thinking. Thinking was good, he reminded himself. It was not thinking about the alternative applications of his research that had started this mess. He looked up at Soundwave. "We need to talk."

Soundwave looked down at him.

Raf took a deep breath. "OK, here's the rundown. This code update should take care of the evil nanites. We reprogram some of them with this, they'll be back to their original programming. They'll start repairing the damage. I also wrote in a conversion code. They come into contact with any evil nanites, they'll initiate a version check and transmit an update. Give a dose of these to everyone who's been exposed and it'll be...a contagious cure, really. Eventually all the evil nanites should be converted, and...everyone should be fixed, if they can be."

Soundwave nodded.

Raf's fingers tightened on his computer. "This'll also revert them back to their usual self-destruct programming. They'll last about twelve hours, then fry themselves. It's for the best. These were only made for treating acute wounds, and I don't want to give you guys any kind of strange cybernetic auto-immune disorders. I...can think of a lot of ways you could turn them back into a weapon...or some kind of super healing persistent infection. I'm sure you've thought it, too. I guess what I'm saying is that I know you have or can get all the pieces to make this really bad." Raf took another deep breath. "I'm asking you not to use them."

Soundwave tilted his head slightly, faceplate spiking once, inscrutably.

"Keep the code for the cure nanites, if you want. Whoever made this stuff might try this again, and you guys should be prepared. If the Autobots and Decepticons both have them, it'll even the playing field." Raf frowned down at his laptop, its screen filled with neatly tiered code. "I never wanted this to be part of the war. It wasn't made to give anyone an advantage. I just...wanted to help." _And I didn't think. Not like a human, evidently._ He'd been around Cybertronians so long that autorepair nanites seemed about as inherently dangerous as commensal bacteria.

And look where that had gotten him. And here he was, trying to think like a Cybertronian soldier.

God, his head hurt.

Raf looked up again, jaw set. "If we both destroy our copies of the weaponized code, we'll be back where we started. That's fair. Just...don't turn this into another kind of weapon. That's my price for this." He tilted his head over at the Decepticon officers, then at Soundwave's own plating, which if he didn't know better would have just looked a bit more pitted and dusty than usual.

It was a ridiculous thing to ask. Soundwave could do whatever he wanted. He likely would.

But Raf had to ask.

He wondered, briefly, what Optimus would have wanted. He'd have to ask. If he got a chance.

Soundwave reached down, flattening his hand, and Raf sighed and stepped into his palm for the lift up to the console. It was about all the response he'd expected.

\------------

It worked. Not on the first try, or the second. But third time had been the charm.

The autorepair calibrator included a tiny nanite isolator, to take and analyze nanite samples from individual mechs. Raf used it to gather an infinitesimally small sample from the growing pits in Soundwave's plating. It took less than a minute for the autorepair calibrator to reprogram the "evil" nanites. Raf looked up at Soundwave. "Got a guinea pig handy?"

He half expected Soundwave to try it out on one of the Decepticons in the cargo bay. After all, Raf had been clear that this new version was untested, untried, to be used at one's own risk, etc. He was _pretty_ sure it would be ok. He'd double-checked the changes that had been made and the ones he'd made in response. The cure nanites shouldn't interfere with a mech's native nanites, but hey, totally experimental messing around with Cybertronian cyberbiology...anything was possible.

Soundwave reached out, pulling the isolator from its bay in the calibrator and cut the field, upending the contents onto his own hand.

Raf held his breath. Then stopped that, because it would take a lot longer than he could hold his breath to see any visible results.

But after an hour, the pits on Soundwave's hand had all but disappeared. The broken fingertip, which had been slowly eating back towards the first joint, lengthened ever so slightly. Raf took another sample from the wound and fistpumped when it came back 100% cure nanites, busily at work.

Soundwave called in a tiny, sparkless maintenance bot, and Raf spread the sample of cure nanites over its hand. They watched on a surveillance monitor as the bot plunged that hand into the quarantined barrel that had started this whole disaster. By the time the bot returned to medbay, every nanite on it was primed for repair.

And Soundwave had checked out on the medbay berth as regaining lost mass, a microgram at a time.

Tired, hungry, and with a caffeine headache from hell, Rafael Esquivel smiled. "Well," he said, "what now?"

Soundwave looked down at him, silent for a long moment. He walked over to the console where Raf had downloaded the weaponized code. He pulled up the file and, with a flurry of skeletal fingers, deleted it.

Raf's smile grew. It didn't mean anything. For all he knew recovering deleted files off of Cybertronian computers was as easy as it was on human computers. But he appreciated the gesture.

Sometimes...you just had to hope.

NOW, Soundwave's faceplate read. YOU LEAVE.

"Oh, good," Raf said, hopping to his feet. "I was hoping you'd say that."

While Soundwave used one of the consoles to remotely program what looked like a small army of maintenance drones to dunk themselves in the cure barrel and wander around the Nemesis, Raf made sure he dusted himself and his gear with the cure nanites, too. No way did he want to carry the evil ones outside with him. He probably wouldn't feel safe until Ratchet had given him a once-over. From a safe distance, of course.

Ratchet. Raf didn't quite feel up to a call (and his phone was running out of charge as it was), but he sent an email to Ratchet, Penny, and Jake: "Crisis averted. Coming home. Details tomorrow."

Almost immediately, Ratchet sent one back: "I had utter faith in your genius. Tell Soundwave to watch the US/Canada border. There's a stormfront coming through."

"Awesome," Raf said, turning his phone so Soundwave could read it. "Flying through WEATHER."

Soundwave laid out his hand for stepping onto, replying in Raf's own voice, "You have too little faith in my genius." Raf stared at him blankly for a long moment. Then something in his too-tired, under-caffeinated brain broke, and he laughed so hard for so long that he missed most of the trip out of the Nemesis.

The night was quiet and bitterly cold, the wind tugging at Raf's shirt and jeans. Raf was grateful for the relative warmth of Soundwave's cockpit, especially since Soundwave granted him the courtesy of transforming first and letting Raf climb in himself.

Once they'd reached cruising altitude, Raf said, "Okay, I have to ask...what are you gonna tell Megatron?"

Raf had been thinking about it ever since they'd taken off. There was a part of him that regretted that he wouldn't get to see the Decepticon high command's faces when they found out a human had saved them. But Raf couldn't think of very many realistic scenarios where he got out of the Nemesis alive. The Decepticons had been quiet lately, but Raf knew that didn't translate into any love for uppity humans. Especially uppity humans who had seen them at their most helpless. Soundwave was doing him a favor by getting him out of there before he finished reviving the Decepticons.

Soundwave hadn't answered him. "Oh, come on," Raf said, suppressing a yawn. "If Megatron's likely to take offense and I need to start watching every car on the street again, I need to know."

YOU DID NOT AID IN THE CURING OF THE NANITE INFECTION.

"Well, that's reassuring."

YOU WERE NOT ON THE NEMESIS. KNOCK OUT WAS ABLE TO FIND THE ROGUE CODE AND REPROGRAM THE NANITES. THE REPROGRAMMING REACTIVATED THE NANITES' LATENT SELF-DESTRUCT PROGRAMS, RESULTING IN HALTING OF DAMAGE, SHORT-TERM ENHANCED HEALING, AND EVENTUAL DESTRUCTION OF ALL ALTERED NANITES ON THE NEMESIS.

That...would work, Raf guessed. Yeah. That could really work. "And Knock Out will go along with this?"

KNOCK OUT WILL GET CREDIT FOR SAVING ENTIRE NEMESIS AND DECEPTICON HIGH COMMAND. WILL HAVE NO OBJECTIONS TO PLAN.

"And he won't get curious as to why you're letting him take the credit?" Raf realized how this sounded and waved a hand. "Just playing devil's advocate here. It's kinda fun."

CURIOSITY IRRELEVANT. INVESTIGATION WILL REVEAL NO CLUES AS TO ACTUAL EVENTS.

"I guess surveillance footage and sensor logs would be easy for you to fake, huh?"

EXTREMELY.

Raf chuckled and sat back in his seat. He hadn't known he was tense until he wasn't.

ASSISTANCE POSSIBLY REQUIRED.

Raf's eyes snapped fully open. They kept drifting shut. "What, again?"

MEGATRON LIKELY TO INVESTIGATE SOURCE OF NANITE INFECTION.

"Makes sense." Something occurred to Raf, and suddenly he was wide awake again. "Wait. Do YOU know who modified the code?" That came out more demanding than Raf meant it to. Oh, who was he kidding, it came out exactly as demanding as he meant it to.

There was a pause, then, DROPKICK'S SQUAD SENT TO INVESTIGATE POSSIBLE MECH RESEARCH FACILITY.

MECH. God. "They're still around? Great."

STILL ACTIVE. STILL UNDER INVESTIGATION BY US GOVERNMENT AND AUTOBOTS. ASSISTANCE REQUIRED: CONVINCE AUTOBOTS NOT TO INVESTIGATE.

Raf stared out the window. They were skirting the stormfront that Ratchet had warned them about. Lightning flickered below them, illuminating the cloudtops Raf could barely see in the darkness. "Because Megatron'll want to pound them himself and we should just get out of the way?"

AFFIRMATIVE.

Megatron would probably kill them. Raf couldn't bring himself to feel bad about that. He supposed that made him a bad person, but he was willing to live with it. "Well, ok, so long as you promise he'll do a good job."

ALSO, IF INVESTIGATION REVEALS AUTOBOT PRESENCE, SUSPICIONS WILL ARISE.

"Oh. Yeah, I get you. Less Autobots anywhere near the evil nanites, the better. Gotcha." Raf stretched as much as he could in the cramped cockpit, trying to relieve a crick in the small of his back. His fingertips brushed the ceiling and he curled them under reflexively, as if he'd touched a stranger accidentally.

A bit later, he asked, quietly, "You really do want peace, don't you? I mean...it'd be easy to restart the war over this, but you keep steering everything away from that."

He didn't get an answer to that one. For the rest of the ride, there was nothing but the hum of the engines, the glow of the instrument panel, and, every now and then, a city's lights laid out in a glittering grid beneath them.

It felt like an answer anyway.

\---------

Soundwave dropped Raf off at the very same bus stop he'd abducted him from sixteen hours earlier. He transformed around his half-asleep passenger, set him down, and was gone before Raf had gotten his balance back.

"You're welcome," Raf muttered up at the night sky, trying to find his keys as he crossed the street. Before he could enter his apartment building, his phone chirped. Fishing it out, he saw a text message from Ratchet that just read: Don't move.

Green light floated around him, coming, apparently, from the two potted plants on either side of his building's front door. Now that he was looking for them, Raf could see the small mechanical boxes hidden under the broad leaves. Raf laughed and obediently didn't move. "Nice, Ratchet."

The green light winked out, and a few seconds later two engines started up further down the street. Raf squinted toward the sound and grinned at the familiar ambulance and the not-so-familiar bright yellow sportscar pulling up at the curb. Bee had evidently taken a new alt form since the last time Raf had seen him. "I guess I'm clean, then?"

"You are," Ratchet said, voice pitched not to carry too loudly on the deserted street. "Though you are CRAWLING with your cure nanites."

Raf rubbed a hand over his arm. "Yeah, thanks for reminding me. I so want a shower it's not even funny."

"You're exhausted," Ratchet said. "We won't keep you. But you are all right?"

Raf smiled. "Yeah, I'm fine. What, you couldn't tell?" He picked the scanners out of the plants and brought them to the curb. Ratchet opened his passenger side door and Raf set them on the seat. He patted Bumblebee's side panel and got a chirped greeting thick with concern and relief in return.

Ratchet harrumphed. "They can't tell me your psychological state. All I could tell was that you are fatigued and not unduly stressed. Everything ended well, I assume?"

"I...think so? I'm pretty sure that we're...back where we started. The Decepticons are going to have this--" he shook the front of his shirt "--version of the nanites, but Soundwave at least appeared to delete all the copies of the weaponized code. Worst case scenario, he was lying and they'll have that, too."

"I doubt it would be useful to them, to be honest. We have the antidote, and if Megatron feels the need to reopen his cyberbiological weapons program, he'd be better off making a variant of cybonic plague or something else that replicates on its own."

"Yeah. Good point," Raf said, yawning hugely.

Ratchet started up his engine. "I'll leave you to your rest. Give us a call tomorrow when you get up, and you can give a detailed report."

Raf saluted lazily. "Sure thing. And thanks, by the way. I don't know what I would have done without you."

Ratchet hmmphed. "You'd have done fine, I imagine. In case you didn't notice, Rafael, I did very little."

Raf started to protest on reflex, but then realized that Ratchet was probably right. "I hope...I hope I did okay. I mean...I'm not a politician or a soldier or leader or anything, and I kinda....had to make a few calls."

"We all do, sooner or later. It's part of being an Autobot," Ratchet said, sounding rather disconcertingly reassuring. For Ratchet. "Good night, Rafael."

"...'night."

Watching Ratchet's tail lights turn the corner, Raf looked down at Bumblebee. "Did he just say that I was...?"

 _boop_

"Aw, shucks."

 _boopbeepboop_

"Okay, now you're just trying to embarrass me."

 _brrrrt_

Raf pushed away from where he'd been leaning against Bumblebee's side. "I notice you're still here."

 _meeboopoopmeepwoopboopwhrrrrrr_

"Well, you're more than welcome to, but I think it'll be ok, really. Soundwave said he was gonna try to leave me out of it completely, and I left way before anyone else woke up."

 _mrrpbeebeep_

"S'okay. I wasn't doing it for the kudos anyway."

 _brrrpboop_

Raf yawned again. "Yeah, going. 'night, Bee."

 **boop!**

Raf fished out his keys and headed up to his apartment. He pulled a canned coffee out of the fridge and slammed the whole thing in an effort to make the caffeine withdrawal SHUT UP and let him sleep. Then he took a long, hot shower wherein he scrubbed everything he could reach twice, then once again for good measure. Once he was done with that, he crawled into bed and was asleep before his head hit the pillow.

When he woke up two hours later from a dream of being slowly eaten alive by something too small to see, he just laid there and panted in the warm darkness. Then, deciding he didn't give a flying leap what his neighbors might think, he put on shoes and padded back outside.

Bee, tucked into the far corner of the apartment building parking lot, opened his door without a sound. Raf put the seat back, wiggled a bit to get comfortable, and fell back to sleep.

He woke in the morning with the sun in his eyes and both his feet completely asleep, but without any more nightmares. Raf counted it a victory.

**Works inspired by this one:**

  * [Good Soldier](https://archiveofourown.org/works/840358) by [flurrybird](https://archiveofourown.org/users/flurrybird/pseuds/flurrybird)




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